Development of an automated DNA sequence variation analysis software and data management package is proposed. The software is aimed at analyzing diploid sequencing and methylation analysis samples from patients in a study population that have been stratified by some defining criteria or phenotype in relation to a disease of interest. The goal of the software is to detect relatively rare sequence variations or methylation state changes which when analyzed for functional effect can be statistically correlated with the phenotype of interest. In this Phase I proposal, we propose to extend an existing database architecture and develop pre-processing software that will characterize all observed variations (including frameshifts) and provide a score related to the likelihood that the observed variation is present in the sample. PROPOSED COMMERCIAL APPLICATION: The pharmaceutical and biotechnology industry is expected to become increasingly reliant in their drug development efforts on the ready identification of new and existing polymorphisms in clinical and other study populations of humans. The software developed using this grant will become centrally important in reliably identifying and assaying polymorphisms from diploid genomic sources.